Protein ungapped extension code. More...
#include <algo/blast/core/ncbi_std.h>#include <algo/blast/core/blast_lookup.h>#include <algo/blast/core/blast_parameters.h>#include <algo/blast/core/blast_extend.h>#include <algo/blast/core/blast_hits.h>#include <algo/blast/core/lookup_wrap.h>#include <algo/blast/core/blast_diagnostics.h>
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Functions | |
| Int2 | BlastAaWordFinder (BLAST_SequenceBlk *subject, BLAST_SequenceBlk *query, BlastQueryInfo *query_info, LookupTableWrap *lookup, Int4 **matrix, const BlastInitialWordParameters *word_params, Blast_ExtendWord *ewp, BlastOffsetPair *offset_pairs, Int4 offset_array_size, BlastInitHitList *init_hitlist, BlastUngappedStats *ungapped_stats) |
| Scan a subject sequence for word hits (blastp) More... | |
| Int2 | BlastRPSWordFinder (BLAST_SequenceBlk *subject, BLAST_SequenceBlk *query, BlastQueryInfo *query_info, LookupTableWrap *lookup, Int4 **matrix, const BlastInitialWordParameters *word_params, Blast_ExtendWord *ewp, BlastOffsetPair *offset_pairs, Int4 offset_array_size, BlastInitHitList *init_hitlist, BlastUngappedStats *ungapped_stats) |
| Scan a subject sequence for word hits (rpsblast and rpstblastn) More... | |
Detailed Description
Protein ungapped extension code.
Definition in file aa_ungapped.h.
Function Documentation
◆ BlastAaWordFinder()
| Int2 BlastAaWordFinder | ( | BLAST_SequenceBlk * | subject, |
| BLAST_SequenceBlk * | query, | ||
| BlastQueryInfo * | query_info, | ||
| LookupTableWrap * | lookup, | ||
| Int4 ** | matrix, | ||
| const BlastInitialWordParameters * | word_params, | ||
| Blast_ExtendWord * | ewp, | ||
| BlastOffsetPair * | offset_pairs, | ||
| Int4 | offset_array_size, | ||
| BlastInitHitList * | init_hitlist, | ||
| BlastUngappedStats * | ungapped_stats | ||
| ) |
Scan a subject sequence for word hits (blastp)
- Parameters
-
subject the subject sequence [in] query the query sequence [in] query_info concatenated query information [in] lookup the lookup table [in] matrix the substitution matrix [in] word_params word parameters, needed for cutoff and dropoff [in] ewp extend parameters, needed for diagonal tracking [in] offset_pairs Array for storing query and subject offsets. [in] offset_array_size the number of elements in each offset array [in] init_hitlist hsps resulting from the ungapped extension [out] ungapped_stats Various hit counts. Not filled if NULL [out]
Definition at line 200 of file aa_ungapped.c.
References Blast_InitHitListSortByScore(), Blast_ExtendWord::diag_table, BLAST_DiagTable::multiple_hits, query, s_BlastAaWordFinder_OneHit(), s_BlastAaWordFinder_TwoHit(), and subject.
Referenced by s_BlastSetUpAuxStructures().
◆ BlastRPSWordFinder()
| Int2 BlastRPSWordFinder | ( | BLAST_SequenceBlk * | subject, |
| BLAST_SequenceBlk * | query, | ||
| BlastQueryInfo * | query_info, | ||
| LookupTableWrap * | lookup, | ||
| Int4 ** | matrix, | ||
| const BlastInitialWordParameters * | word_params, | ||
| Blast_ExtendWord * | ewp, | ||
| BlastOffsetPair * | offset_pairs, | ||
| Int4 | offset_array_size, | ||
| BlastInitHitList * | init_hitlist, | ||
| BlastUngappedStats * | ungapped_stats | ||
| ) |
Scan a subject sequence for word hits (rpsblast and rpstblastn)
- Parameters
-
subject the subject sequence [in] query the query sequence [in] query_info concatenated query information [in] lookup the lookup table [in] matrix the substitution matrix [in] word_params word parameters, needed for cutoff and dropoff [in] ewp extend parameters, needed for diagonal tracking [in] offset_pairs Array for storing query and subject offsets. [in] offset_array_size the number of elements in each offset array [in] init_hitlist hsps resulting from the ungapped extension [out] ungapped_stats Various hit counts. Not filled if NULL [out]
Definition at line 238 of file aa_ungapped.c.
References BLAST_FrameToContext(), Blast_InitHitListSortByScore(), context, BlastUngappedCutoffs::cutoff_score, BlastInitialWordParameters::cutoffs, Blast_ExtendWord::diag_table, eBlastTypeRpsTblastn, BLAST_DiagTable::multiple_hits, NUM_FRAMES, query, s_BlastRPSWordFinder_OneHit(), s_BlastRPSWordFinder_TwoHit(), subject, and BlastUngappedCutoffs::x_dropoff.
Referenced by s_BlastSetUpAuxStructures().
